The computer controlled analytical electron microscope developed jointly by BEIB and CSL, DCRT, provides a unique tool for measuring sub-cellular elemental distributions with a resolution of some 10 nm. Experiments have been carried out to test the capabilities of the instrumentation and to develop further the methodologies for analysis. Nitrogen electron energy loss images have been recorded from cryofixed pancreas beta and adrenol chromaffin cells. Calcium and nitrogen maps have been obtained from rapidly frozen and freeze substituted spinal cord neurons, treated with potassium and sodium glutamate to produce calcium deposits in their mitochrondria. In these images it has been found crucial to model the spectral background correctly and a one-parameter fit, which is often assumed, in general leads to artifacts despite an apparent improvement in signal-to-noise ratio. Ratio maps of nitrogen to phosphorus or sulphur can be obtained from the appropriate x-ray images and these ratios can be related to the biochemical constituents of organelles. New software controlling the DeAnza image display system allows quantitation of the chemical maps. Thus, for example, the ratio image of two energy loss maps eliminates, to first order, the effects of plural scattering. It has been possible to quantitate x-ray microanalysis in thin cryosections by using inelastic electron as measured by EELS to determine the mass per unit area in 100 nm diameter regions at extremely low dose (approximately 100 electrons nm to the-2). This enables quantitative measurements to be made from hydrated cryosections, including an estimate of the water content. Forthcoming improvements in the electron energy loss spectrometer should provide increased sensitivity and allow annular dark field STEM imaging to be carried out simultaneously. It will also be possible to perform Z-contrast imaging in suitably thin samples. This new contrast mode is predicted to depend only on local mean atomic number and thickness effects are cancelled.